Microbial 'omics


Brought to you by

Table of Contents

DB

A DB-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

Back to the main page of anvi’o programs and artifacts.

Provided by

anvi-gen-contigs-database

Required or used by

anvi-analyze-synteny anvi-cluster-contigs anvi-display-contigs-stats anvi-display-structure anvi-estimate-genome-completeness anvi-estimate-kegg-metabolism anvi-estimate-scg-taxonomy anvi-export-contigs anvi-export-functions anvi-export-gene-calls anvi-export-locus anvi-export-misc-data anvi-export-splits-and-coverages anvi-gen-fixation-index-matrix anvi-gen-gene-level-stats-databases anvi-gen-structure-database anvi-gen-variability-profile anvi-get-codon-frequencies anvi-get-sequences-for-gene-calls anvi-get-sequences-for-hmm-hits anvi-get-short-reads-from-bam anvi-get-short-reads-mapping-to-a-gene anvi-import-collection anvi-import-functions anvi-import-misc-data anvi-import-taxonomy-for-genes anvi-inspect anvi-interactive anvi-merge anvi-profile anvi-refine anvi-run-hmms anvi-run-kegg-kofams anvi-run-ncbi-cogs anvi-run-pfams anvi-run-scg-taxonomy anvi-scan-trnas anvi-search-functions anvi-split anvi-summarize

Description

An anvi’o database that contains key information associated with your sequences.

In a way, an anvi’o contigs database is a modern, more talented form of a FASTA file, where you can store additional information about your sequences in it and others can query and use it. Information storage and access is primarily done by anvi’o programs, however, it can also be done through the command line interface or programmatically.

The information a contigs database contains about its sequences include the positions of open reading frames, tetra-nucleotide frequencies, functional and taxonomic annotations, information on individual nucleotide or amino acid positions, and more.

Key programs that populate an anvi’o contigs database with essential information include anvi-run-hmms, anvi-run-scg-taxonomy, and anvi-scan-trnas.

Once an anvi’o contigs database is generated and populated with information, it is always a good idea to run anvi-display-contigs-stats to see a numerical summary of its contents.

Other essential programs that read from a contigs database and yield key information include anvi-estimate-genome-completeness, anvi-get-sequences-for-hmm-hits, anvi-estimate-scg-taxonomy.

Edit this file to update this information.